Dengue (DENV) and Zika (ZIKV) viruses are clinically important members of the Flaviviridae family with an 11 kb positive strand RNA genome that folds to enable virus function. Here, we perform structure and interaction mapping on four DENV and ZIKV strains inside virions and in infected cells. Comparative analysis of SHAPE reactivities across serotypes nominates potentially functional regions that are highly structured, conserved, and contain low synonymous mutation rates. Interaction mapping by SPLASH identifies many pair-wise interactions, 40% of which form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared interactions between serotypes reveals a conserved macro-organization whereby interactions can be preserved at physical locations beyond sequence identities. We further observe that longer-range interactions are preferentially disrupted inside cells, and show the importance of new interactions in virus fitness. These findings deepen our understanding of Flavivirus genome organization and serve as a resource for designing therapeutics in targeting RNA viruses.

Biological invasions that involve well-documented rapid adaptations to new environments provide unequalled opportunities for testing evolutionary hypotheses. Mikania micrantha Kunth (Asteraceae), a perennial herbaceous vine native to tropical Central and South America, successfully invaded tropical Asia in the early 20th century. It is regarded as one of the most aggressive weeds in the world. To elucidate the molecular and evolutionary processes underlying this invasion, we extensively sampled this weed throughout its invaded range in South-East and South Asia and surveyed its genetic structure using variants detected from population transcriptomics. Clustering results suggest that more than one source population contributed to this invasion. Computer simulations using genomewide genetic variation support a scenario of admixture and founder events during invasion. The genes differentially expressed between native and invasive populations were found to be involved in oxidative and high light intensity stress responses, pointing to a possible ecological mechanism of adaptation. Our results provide a foundation for further detailed mechanistic and population studies of this ecologically and economically important invasion. This line of research promises to provide new mitigation strategies for invasive species as well as insights into mechanisms of adaptation.

Membrane-less scenarios that involve liquid−liquid phase separation (coacervation) provide clues for how protocells might emerge. Here, we report a versatile approach to construct coacervates by mixing fatty acid with biomolecule dopamine as the protocell model. The coacervate droplets are easily formed over a wide range of concentrations. The solutes with different interaction characteristics, including cationic, anionic, and hydrophobic dyes, can be well concentrated within the coacervates. In addition, reversible self-assemblies of the coacervates can be controlled by concentration, pH, temperature, salinity, and bioreaction realizing cycles between compartmentalization and noncompartmentalization. Through in situ dopamine polymerization, the stability of coacervate droplets is significantly improved, leading to higher resistance toward external factors. Therefore, the coacervates based on fatty acid and dopamine could serve as a bottom-up membrane-less protocell model that provides the links between the simple (small molecule) and complex (macromolecule) systems in the process of cell evolution.